Category Archives: ISAcreator configurator

For browsing and querying OLS and BioPortal seamlessly, ISAcreator and it’s associated configurator have done much to make life easier for it’s users.

ISAcreator configurator and it’s use for ontologies

ISAcreator Configurator is a tool used by community experts or curators to detail the Minimum Information (via MIBBI for instance) that users should enter to describe their experiment. As part of this, curators can define which fields (e.g. Sample Name) are required, whether or not they require ontology terms and if so, which ontologies (and parts of the ontologies) users should be pointed to.

ISAcreator Configurator – allows curators to define ‘checklists’: these are the fields required to describe an experiment from start to finish.

The ISAcreator configurator provides both the ability to browse ontologies and to search them, so as to allow curators to select which ontologies and which parts of these ontologies should be suggested to users whenever they annotate a field in the ISAcreator.

Browsing ontologies

Users can browse ontologies in OLS and BioPortal via an easy to use GUI. The browsing is done on the fly by accessing hierarchy web services from both the OLS and BioPortal. An extensible code base means that other ontology resource (should they become available) can be added at any point.

Browse ChEBI from OLS

Browsing OBI (Ontology for Biomedical Investigations) from BioPortal

Search within ontologies

Search within ontologies

Users can search within ontologies and then locate the ontology in the entire ontology hierarchy. This functionality is provided to aid curators in finding the appropriate branch of an ontology to restrict users to.

ISAcreator and how it makes ontology selection easier for users

ISAcreator is a tool used by the community who often don’t know much about ontologies or the minimum information required to describe an experiment. The ISAcreator configurator produces XML describing the minimum information and the ontologies to use so that users need not worry about what to enter.

ISAcreator’s main menu

The user interface needs to be easy to use, and ontology selection should be seamless. The user needs not know which ontology resource they are browsing, but ontologies should be presented to them in a way which makes selection straightforward. ISAcreator achieves this by automatically prompting users for ontology terms whenever they are set to be required by the ISAcreator configurator.

Users are automatically prompted for Ontology terms

Users are presented with the full search result from both OLS and Bioportal in a standard form.

In summary, the functionalities inside both ISAcreator and it’s associated configurator make browsing and searching both OLS and BioPortal much simpler for users! An API with many advanced functionalities, building upon BioPortal and OLS services will be released soon as well as a standalone ontology browser and searcher!